These files are on my USB flash drive. I can't view them with Dolphin, but I can view them in the terminal. I tried to copy them, but I failed? Virus? Is it OK to format the USB flash drive completely if I can?

what was the command you used in the terminal? it looks like you did ls /dev which isn't your flash drive but the root device location. your flash drive should be mounted at /media/$USER/flashdrivename in 13.04 or /media/flashdrivename in earlier versions of ubuntu
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amcAug 25 '13 at 15:11

I agree with the other answer. Looks like these are devices & a few apps like alarm on the system. If it's nothing you need on that flashdrive, you should format it just to be safe since you said you cleared few viruses.
On windows goto start->type diskpart & select diskpart.exe